X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=commandfactory.cpp;h=02af6767b00b724459c054839b789798f4b295f7;hb=2ecee16fec29d4c525f740ec19b27962ca09c050;hp=527f7bfe4fddf6ecf1ddce45ab7c93a161f52ad1;hpb=aa23898d895a8c04cc4582a8809343df0aef6622;p=mothur.git diff --git a/commandfactory.cpp b/commandfactory.cpp index 527f7bf..02af676 100644 --- a/commandfactory.cpp +++ b/commandfactory.cpp @@ -8,9 +8,6 @@ */ #include "command.hpp" -#include "readdistcommand.h" -#include "readtreecommand.h" -#include "readotucommand.h" #include "clustercommand.h" #include "collectcommand.h" #include "collectsharedcommand.h" @@ -131,6 +128,12 @@ #include "pcrseqscommand.h" #include "createdatabasecommand.h" #include "makebiomcommand.h" +#include "getcoremicrobiomecommand.h" +#include "listotulabelscommand.h" +#include "getotulabelscommand.h" +#include "removeotulabelscommand.h" +#include "makecontigscommand.h" +#include "loadlogfilecommand.h" /*******************************************************/ @@ -163,9 +166,6 @@ CommandFactory::CommandFactory(){ append = false; //initialize list of valid commands - commands["read.dist"] = "read.dist"; - commands["read.otu"] = "read.otu"; - commands["read.tree"] = "read.tree"; commands["make.shared"] = "make.shared"; commands["bin.seqs"] = "bin.seqs"; commands["get.oturep"] = "get.oturep"; @@ -283,6 +283,13 @@ CommandFactory::CommandFactory(){ commands["pcr.seqs"] = "pcr.seqs"; commands["create.database"] = "create.database"; commands["make.biom"] = "make.biom"; + commands["get.coremicrobiome"] = "get.coremicrobiome"; + commands["list.otulabels"] = "list.otulabels"; + commands["get.otulabels"] = "get.otulabels"; + commands["remove.otulabels"] = "remove.otulabels"; + commands["make.contigs"] = "make.contigs"; + commands["load.logfile"] = "load.logfile"; + commands["make.table"] = "make.table"; commands["quit"] = "MPIEnabled"; } @@ -372,10 +379,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){ else { optionString += "inputdir=" + inputDir; } } - if(commandName == "read.dist") { command = new ReadDistCommand(optionString); } - else if(commandName == "read.otu") { command = new ReadOtuCommand(optionString); } - else if(commandName == "read.tree") { command = new ReadTreeCommand(optionString); } - else if(commandName == "cluster") { command = new ClusterCommand(optionString); } + if(commandName == "cluster") { command = new ClusterCommand(optionString); } else if(commandName == "unique.seqs") { command = new DeconvoluteCommand(optionString); } else if(commandName == "parsimony") { command = new ParsimonyCommand(optionString); } else if(commandName == "help") { command = new HelpCommand(optionString); } @@ -479,7 +483,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){ else if(commandName == "make.shared") { command = new SharedCommand(optionString); } else if(commandName == "get.commandinfo") { command = new GetCommandInfoCommand(optionString); } else if(commandName == "deunique.tree") { command = new DeuniqueTreeCommand(optionString); } - else if(commandName == "count.seqs") { command = new CountSeqsCommand(optionString); } + else if((commandName == "count.seqs") || (commandName == "make.table")) { command = new CountSeqsCommand(optionString); } else if(commandName == "count.groups") { command = new CountGroupsCommand(optionString); } else if(commandName == "clear.memory") { command = new ClearMemoryCommand(optionString); } else if(commandName == "summary.tax") { command = new SummaryTaxCommand(optionString); } @@ -493,6 +497,12 @@ Command* CommandFactory::getCommand(string commandName, string optionString){ else if(commandName == "pcr.seqs") { command = new PcrSeqsCommand(optionString); } else if(commandName == "create.database") { command = new CreateDatabaseCommand(optionString); } else if(commandName == "make.biom") { command = new MakeBiomCommand(optionString); } + else if(commandName == "get.coremicrobiome") { command = new GetCoreMicroBiomeCommand(optionString); } + else if(commandName == "list.otulabels") { command = new ListOtuLabelsCommand(optionString); } + else if(commandName == "get.otulabels") { command = new GetOtuLabelsCommand(optionString); } + else if(commandName == "remove.otulabels") { command = new RemoveOtuLabelsCommand(optionString); } + else if(commandName == "make.contigs") { command = new MakeContigsCommand(optionString); } + else if(commandName == "load.logfile") { command = new LoadLogfileCommand(optionString); } else { command = new NoCommand(optionString); } return command; @@ -524,10 +534,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str else { optionString += "inputdir=" + inputDir; } } - if(commandName == "read.dist") { pipecommand = new ReadDistCommand(optionString); } - else if(commandName == "read.otu") { pipecommand = new ReadOtuCommand(optionString); } - else if(commandName == "read.tree") { pipecommand = new ReadTreeCommand(optionString); } - else if(commandName == "cluster") { pipecommand = new ClusterCommand(optionString); } + if(commandName == "cluster") { pipecommand = new ClusterCommand(optionString); } else if(commandName == "unique.seqs") { pipecommand = new DeconvoluteCommand(optionString); } else if(commandName == "parsimony") { pipecommand = new ParsimonyCommand(optionString); } else if(commandName == "help") { pipecommand = new HelpCommand(optionString); } @@ -630,7 +637,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str else if(commandName == "make.shared") { pipecommand = new SharedCommand(optionString); } else if(commandName == "get.commandinfo") { pipecommand = new GetCommandInfoCommand(optionString); } else if(commandName == "deunique.tree") { pipecommand = new DeuniqueTreeCommand(optionString); } - else if(commandName == "count.seqs") { pipecommand = new CountSeqsCommand(optionString); } + else if((commandName == "count.seqs") || (commandName == "make.table")) { pipecommand = new CountSeqsCommand(optionString); } else if(commandName == "count.groups") { pipecommand = new CountGroupsCommand(optionString); } else if(commandName == "clear.memory") { pipecommand = new ClearMemoryCommand(optionString); } else if(commandName == "summary.tax") { pipecommand = new SummaryTaxCommand(optionString); } @@ -644,6 +651,12 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str else if(commandName == "pcr.seqs") { pipecommand = new PcrSeqsCommand(optionString); } else if(commandName == "create.database") { pipecommand = new CreateDatabaseCommand(optionString); } else if(commandName == "make.biom") { pipecommand = new MakeBiomCommand(optionString); } + else if(commandName == "get.coremicrobiome") { pipecommand = new GetCoreMicroBiomeCommand(optionString); } + else if(commandName == "list.otulabels") { pipecommand = new ListOtuLabelsCommand(optionString); } + else if(commandName == "get.otulabels") { pipecommand = new GetOtuLabelsCommand(optionString); } + else if(commandName == "remove.otulabels") { pipecommand = new RemoveOtuLabelsCommand(optionString); } + else if(commandName == "make.contigs") { pipecommand = new MakeContigsCommand(optionString); } + else if(commandName == "load.logfile") { pipecommand = new LoadLogfileCommand(optionString); } else { pipecommand = new NoCommand(optionString); } return pipecommand; @@ -661,10 +674,7 @@ Command* CommandFactory::getCommand(string commandName){ try { delete shellcommand; //delete the old command - if(commandName == "read.dist") { shellcommand = new ReadDistCommand(); } - else if(commandName == "read.otu") { shellcommand = new ReadOtuCommand(); } - else if(commandName == "read.tree") { shellcommand = new ReadTreeCommand(); } - else if(commandName == "cluster") { shellcommand = new ClusterCommand(); } + if(commandName == "cluster") { shellcommand = new ClusterCommand(); } else if(commandName == "unique.seqs") { shellcommand = new DeconvoluteCommand(); } else if(commandName == "parsimony") { shellcommand = new ParsimonyCommand(); } else if(commandName == "help") { shellcommand = new HelpCommand(); } @@ -767,7 +777,7 @@ Command* CommandFactory::getCommand(string commandName){ else if(commandName == "make.shared") { shellcommand = new SharedCommand(); } else if(commandName == "get.commandinfo") { shellcommand = new GetCommandInfoCommand(); } else if(commandName == "deunique.tree") { shellcommand = new DeuniqueTreeCommand(); } - else if(commandName == "count.seqs") { shellcommand = new CountSeqsCommand(); } + else if((commandName == "count.seqs") || (commandName == "make.table")) { shellcommand = new CountSeqsCommand(); } else if(commandName == "count.groups") { shellcommand = new CountGroupsCommand(); } else if(commandName == "clear.memory") { shellcommand = new ClearMemoryCommand(); } else if(commandName == "summary.tax") { shellcommand = new SummaryTaxCommand(); } @@ -781,6 +791,12 @@ Command* CommandFactory::getCommand(string commandName){ else if(commandName == "pcr.seqs") { shellcommand = new PcrSeqsCommand(); } else if(commandName == "create.database") { shellcommand = new CreateDatabaseCommand(); } else if(commandName == "make.biom") { shellcommand = new MakeBiomCommand(); } + else if(commandName == "get.coremicrobiome") { shellcommand = new GetCoreMicroBiomeCommand(); } + else if(commandName == "list.otulabels") { shellcommand = new ListOtuLabelsCommand(); } + else if(commandName == "get.otulabels") { shellcommand = new GetOtuLabelsCommand(); } + else if(commandName == "remove.otulabels") { shellcommand = new RemoveOtuLabelsCommand(); } + else if(commandName == "make.contigs") { shellcommand = new MakeContigsCommand(); } + else if(commandName == "load.logfile") { shellcommand = new LoadLogfileCommand(); } else { shellcommand = new NoCommand(); } return shellcommand;